[gmx-users] pdb2gmx of nucleic acids with ffamber03 force field

MARIA ICIAR FRADES ALZUETA mariaiciar.frades at ehu.es
Wed Aug 31 16:43:19 CEST 2011

Dear all,

I am trying to pdb2gmx a a pdb file gcaa.pdb having nucleic acids  
using amber force field 03:
pdb2gmx -ff amber03 -f gcaa.pdb -o rna.pdb -p rna.top -water tip3p

I have two questions:
The ffamber03.rtp file specifies that O2 from should be O to be  
recognized by the rtp file. When one substitutes this atom the program  
Fatal error:
Atom O in residue RC 4 was not found in rtp entry RC with 31 atoms
while sorting atoms.

Keeping the original pdb O2 works fine, althought O2 is not in the  
ffamber03.rtp  file. Is this fine?

When doing: editconf -f gcaa.pdb -o this.pdb
The residues named H2'1 as mapped in the .rtp file they became 1H2'.  
The pdb2gmx works fine but I do not know how it works if the new 1H2'  
is not in the ffamber03.rtp file.

Itziar Frades

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